Uusi rekombinanttialalryhmä käsittelyyn kuusi tuntia siten

 klo 16:09,  25.5. 2023 Ruotsin aikaa.

 

https://github.com/cov-lineages/pango-designation/issues/2019 

Title:

Nimim. Josette S...

Potential XBB.1.9.1/(1.9.2 or XBB.1.22.2) recombinant (56 samples) with a branch with S:Y200C and S:T487R (11 samples) #2019

Description: XBB.1.9.1/XBB.1.9.2 recombinant, with a big (mostly South Korean) branch with ORF8:I74V and a smaller branch which first gained S:Y200C and an ORF3a frameshift and after that a small saltation with S:478R (Australia, USA, the Netherlands, China)
Private mutations: C6285T, G12907A, C28770T
Breakpoint: between nucleotide 16878 and 27507
Earliest sequence: 2023-03-10 from England (with S:Y200C and ORF3a frameshift)
2023-03-22 from South Korea (with ORF8:I74V)
2023-03-29 from NSW/Australia (with extra small saltation with S:478R)
Most recent sequence: 2023-05-15 from Fujian/China
Countries circulating: South Korea 31, Australia/USA 7, China 3, Japan/England 2, the Netherlands/Indonesia/Ireland/Taiwan 1
GISAID query: C6285T, C11956T, A27507C
CovSpectrum query: https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?nucMutations=C6285T%2CC11956T%2CA27507C&nextcladePangoLineage1=xbb.1.9.1*&
to which S:K478R or A28113G could be added to find the various sublineages.
Usher tree: (Figure)

Please note that because the XBB.1.9.2. part only differs one mutation from XBB.1.9.1 (A27507C), convergent evolution cannot be ruled out. But because of the extra private mutations, I think recombination is more likely.

Please see this issue from Fede for more background info and discussion: sars-cov-2-variants/lineage-proposals#73.  

XBB.1.9.1 with S:Y200C and S:T478R, Orf1b:H641Q (NSP12_H650Q) in the branch with Orf1a:T2007I (NSp3_T1189I) and N:T166I (9 sequences) #73

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(Tässä asinkäsitelyss ä#73 annettiin seuraavat suuntaviivat: Labels : 

Labels

Convergent evolution . 

 Lineages with convergent mutations. 

 Rapid review needed

Green light to be proposed 

 (Sitten asia siirtyi tänään  25.5. 2023 nopeaan käsittelyyn):

Comments:

FedeGueli,: Thx  JosetteS....

"To track the smaller sublineage of this one with S:K478R i suggest this query :A22161G,C15390A, T26457C, G12907A.

cc  (Masters: @corneliusroemer @InfrPopGen @AngieHinrichs @thomaspeacock
My personal suggestion is a rapid review followed eventually by a designation of ( 'XC?' and .1 and .2 )"

(More comments 4 hours ago)

avi... "A27507C is also in AY.25 and XBB.1.22.2.".

JosetteS...

"Indeed, avi.. I checked and it might have recombined with XBB.1.22.2 as well.

It is the same from G15451A (ORF:G662S) and forward. XBB.1.22.2 does have C15237T, which this recombinant and XBB.1.9.1/2 do not have. So, the breakpoint would be after that in case it recombined with XBB.1.22.2.

I do see 5 XBB.1.9.2 with C28770T, while I see no XBB.1.22.2 with it, which might make it sightly more likely that it recombined with XBB.1.9.2.

The Delta's with A27507C look very different, of course.

Thank you! I will adjust title." 

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